5 The Sargasso Sea Experiment The Power of Environmental MetagenomicsYielded a Total of Over 1 billion Base Pairs of Non-Redundant SequenceDisplayed the Gene Content, Diversity, & Relative Abundance of the OrganismsSequences from at Least 1800 Genomic Species, including 148 Previously UnknownIdentified over 1.2 Million Unknown GenesJ. Craig Venter, et al.Science2 April 2004:Vol. 304.ppMODIS-Aqua satellite image of ocean chlorophyll in the Sargasso Sea grid about the BATS site from 22 February 2003

6 CAMERA will include All Sorcerer II Metagenomic DataMarine Genome Sequencing Project Measuring the Genetic Diversity of Ocean MicrobesCAMERA will include All Sorcerer II Metagenomic Data

7 Much of Genome Work Has Occurred in AnimalsEvolution is the Principle of Biological Systems: Most of Evolutionary Time Was in the Microbial WorldYou Are HereMuch of Genome Work Has Occurred in AnimalsSource: Carl Woese, et al

8 Major New Science Challenge: Understanding the Transition from Collective to Species Evolution“Bacteria naturally reside in communities, in ecosystems. It is hard to find a bacterial niche that does not comprise hundreds or thousands of different species, all interacting in intricate delicate ways, to make a fascinatingly complex and stable whole.”“In an era of rampant horizontal gene transfer, organismal evolution would be basically collective. It is the community of organisms that evolves, not the various individual organismal types.”“This shift from a primitive genetic free-for-all to modern organisms must by all account have been one of the most profound happenings in the whole of evolutionary history.”--Carl Woese , Evolving Biological Organization in Microbial Phylogeny and Evolution, ed. Jan Sapp (2005)

10 Metagenomics Will Couple to Earth Observations Which Add Several TBs/DaySource: Glenn Iona, EOSDIS Element EvolutionTechnical Working Group January 6-7, 2005

11 Performance per Dollar SpentOptical Networks Are Becoming the 21st Century Cyberinfrastructure DriverOptical Fiber(bits per second)(Doubling time 9 Months)Data Storage(bits per square inch)(Doubling time 12 Months)Performance per Dollar SpentSilicon Computer Chips(Number of Transistors)(Doubling time 18 Months)12345Number of YearsScientific American, January 2001

12 Internet2 Backbone is 10,000 Mbps! Throughput is < 0.5% to End UserChallenge: Average Throughput of NASA Data Products to End User is < 50 MbpsTestedOctober 2005Internet2 Backbone is 10,000 Mbps!Throughput is < 0.5% to End User

15 Lambdas Give End Users Sustained ~ 10 Gbps Data Flow RatesGSFC Scientific and Engineering Network (SEN)Mrtg-based `Daily' Graph (5 Minute Average)Bits per second In and OutOn Selected InterfacesOn August 5, 2005, GSFC’s Bill Fink simultaneously conducted two 15-minute-duration UDP-based 4.5-Gbps flow tests, with one flow between GSFC-UCSD and the other between GSFC-StarLight/Chicago. This filled both the NLR/WASH-STAR and DRAGON/channel49 lambdas to 90% of capacity. Flows were also tested in both directions. He measured greater than 9-Gbps aggregate in each direction and no-to-negligible packet losses.DRAGON 10Gig DWDM XFP5 August 2005200 Times Faster Than Standard Internet2!chance1 10Gig (eth1 IntelPro/10GbE)5 August 2005chance2 10Gig (eth1 IntelPro/10GbE)5 August 2005Source: Pat Gary, NASA GSFC15

25 The Bioinformatics Core of the Joint Center for Structural Genomics will be Housed in the BuildingExtremely Thermostable -- Useful for ManyIndustrial Processes (e.g. Chemical and Food)173 Structures (122 from JCSG)Determining the Protein Structures of the Thermotoga Maritima Genome122 T.M. Structures Solved by JCSG (75 Unique In The PDB)Direct Structural Coverage of 25% of the Expressed Soluble ProteinsProbably Represents the Highest Structural Coverage of Any OrganismSource: John Wooley, UCSD

26 Located in Calit2@UCSD BuildingProviding Integrated Grid Software and Infrastructure for Multi-Scale BioModelingNational Biomedical Computation Resourcean NIH supported resource centerLocated in BuildingGrid and Cluster Computing ApplicationsInfrastructureRocks Grid of ClustersAPBSContinuityGtomo2TxBRAutodockGAMESSQMViewBiology drivenScience has top priorityInfrastructure supportPortable solution packageBalance technology development and scientific discoveryMix production software and new technology frameworkProductive and future proofAPBS image: CCMV capsid electrostatic potential mapped on the solvent-accessible molecular surfaceZhang, D., R. Konecny, N.A. Baker, J.A. McCammon. Electrostatic Interaction between RNA and Protein Capsid in CCMV Simulated by a Coarse-grain RNA model and a Monte Carlo Approach. Biopolymers, 75(4), (2004). [link]Abstract: Although many viruses have been crystallized and the protein capsid structures have been determined by x-ray crystallography, the nucleic acids often cannot be resolved. This is especially true for RNA viruses. The lack of information about the conformation of DNA/RNA greatly hinders our understanding of the assembly mechanism of various viruses. Here we combine a coarse-grain model and a Monte Carlo method to simulate the distribution of viral RNA inside the capsid of cowpea chlorotic mottle virus. Our results show that there is very strong interaction between the N-terminal residues of the capsid proteins, which are highly positive charged, and the viral RNA. Without these residues, the binding energy disfavors the binding of RNA by the capsid. The RNA forms a shell close to the capsid with the highest densities associated with the capsid dimers. These high-density regions are connected to each other in the shape of a continuous net of triangles. The overall icosahedral shape of the net overlaps with the capsid subunit icosahedral organization. Medium density of RNA is found under the pentamers of the capsid. These findings are consistent with experimental observations.Figure 3. The electrostatic potential mapped on the solvent-accessible molecular surface of the capsid viewed from outside (a) and inside (b). The color bar is the same for both images.GAMESS/QMView Lepitopterene MoleculeAutodock: Andy’s lab new paper using APBS, Autodock in J. Med. ChemNonhomogeneous Epicardial Strain Measurements of Anterior LV During Acute Myocardial IschemiaRich ClientsWeb PortalGrid Middlewareand Web ServicesWorkflowAPBSCommandMiddlewarePMV ADTVisionTelescience PortalContinuity